Multiple sequence alignment - TraesCS4A01G288400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G288400 chr4A 100.000 3905 0 0 1 3905 593291058 593287154 0.000000e+00 7212
1 TraesCS4A01G288400 chr4A 80.240 334 30 18 3597 3905 593297406 593297728 6.570000e-53 219
2 TraesCS4A01G288400 chr4D 92.073 2397 115 31 834 3189 10389992 10387630 0.000000e+00 3304
3 TraesCS4A01G288400 chr4D 93.326 1948 80 23 1007 2929 10640642 10642564 0.000000e+00 2832
4 TraesCS4A01G288400 chr4D 89.396 613 37 3 1 585 10393994 10393382 0.000000e+00 747
5 TraesCS4A01G288400 chr4D 89.020 510 35 6 2792 3286 10643579 10644082 2.580000e-171 612
6 TraesCS4A01G288400 chr4D 78.972 856 123 34 3078 3903 10386951 10386123 7.430000e-147 531
7 TraesCS4A01G288400 chr4D 84.808 520 34 12 1 475 10408341 10407822 7.590000e-132 481
8 TraesCS4A01G288400 chr4D 89.375 320 19 7 2623 2933 10385039 10384726 4.730000e-104 388
9 TraesCS4A01G288400 chr4D 81.902 326 22 18 3606 3905 10405993 10406307 1.400000e-59 241
10 TraesCS4A01G288400 chr4D 81.098 328 23 20 3606 3905 10412695 10413011 3.930000e-55 226
11 TraesCS4A01G288400 chr4D 87.898 157 11 4 3749 3905 10383673 10383525 1.110000e-40 178
12 TraesCS4A01G288400 chr4D 89.024 82 8 1 3025 3105 10643495 10643576 2.480000e-17 100
13 TraesCS4A01G288400 chr4B 92.881 2079 100 26 1067 3111 20001197 20003261 0.000000e+00 2976
14 TraesCS4A01G288400 chr4B 85.000 340 43 8 2965 3301 19986187 19985853 4.830000e-89 339
15 TraesCS4A01G288400 chr4B 86.920 237 16 10 19 242 19998101 19998335 6.480000e-63 252
16 TraesCS4A01G288400 chr4B 80.117 171 26 4 63 233 19999759 19999921 1.910000e-23 121
17 TraesCS4A01G288400 chr5D 79.813 857 126 30 1099 1931 501095775 501096608 7.270000e-162 580
18 TraesCS4A01G288400 chr5D 80.848 731 127 10 2046 2765 501096768 501097496 2.630000e-156 562
19 TraesCS4A01G288400 chr5B 81.754 707 112 13 2072 2765 622605461 622606163 3.380000e-160 575
20 TraesCS4A01G288400 chr3A 79.872 780 133 20 1151 1924 609688692 609687931 2.050000e-152 549
21 TraesCS4A01G288400 chr3A 84.112 535 79 6 2064 2595 609687746 609687215 2.690000e-141 512
22 TraesCS4A01G288400 chr5A 80.583 721 123 13 2064 2771 626119928 626119212 1.230000e-149 540
23 TraesCS4A01G288400 chr7D 80.305 721 122 15 2064 2768 591813570 591812854 9.610000e-146 527
24 TraesCS4A01G288400 chr3D 79.076 779 141 15 1151 1924 466680044 466679283 2.080000e-142 516
25 TraesCS4A01G288400 chr3B 83.925 535 80 6 2064 2595 620454921 620454390 1.250000e-139 507
26 TraesCS4A01G288400 chr1B 81.100 582 98 11 1138 1710 121178470 121179048 4.600000e-124 455
27 TraesCS4A01G288400 chr1D 80.298 604 108 9 1138 1731 77650298 77650900 2.770000e-121 446


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G288400 chr4A 593287154 593291058 3904 True 7212.000000 7212 100.000000 1 3905 1 chr4A.!!$R1 3904
1 TraesCS4A01G288400 chr4D 10640642 10644082 3440 False 1181.333333 2832 90.456667 1007 3286 3 chr4D.!!$F3 2279
2 TraesCS4A01G288400 chr4D 10383525 10393994 10469 True 1029.600000 3304 87.542800 1 3905 5 chr4D.!!$R2 3904
3 TraesCS4A01G288400 chr4D 10407822 10408341 519 True 481.000000 481 84.808000 1 475 1 chr4D.!!$R1 474
4 TraesCS4A01G288400 chr4B 19998101 20003261 5160 False 1116.333333 2976 86.639333 19 3111 3 chr4B.!!$F1 3092
5 TraesCS4A01G288400 chr5D 501095775 501097496 1721 False 571.000000 580 80.330500 1099 2765 2 chr5D.!!$F1 1666
6 TraesCS4A01G288400 chr5B 622605461 622606163 702 False 575.000000 575 81.754000 2072 2765 1 chr5B.!!$F1 693
7 TraesCS4A01G288400 chr3A 609687215 609688692 1477 True 530.500000 549 81.992000 1151 2595 2 chr3A.!!$R1 1444
8 TraesCS4A01G288400 chr5A 626119212 626119928 716 True 540.000000 540 80.583000 2064 2771 1 chr5A.!!$R1 707
9 TraesCS4A01G288400 chr7D 591812854 591813570 716 True 527.000000 527 80.305000 2064 2768 1 chr7D.!!$R1 704
10 TraesCS4A01G288400 chr3D 466679283 466680044 761 True 516.000000 516 79.076000 1151 1924 1 chr3D.!!$R1 773
11 TraesCS4A01G288400 chr3B 620454390 620454921 531 True 507.000000 507 83.925000 2064 2595 1 chr3B.!!$R1 531
12 TraesCS4A01G288400 chr1B 121178470 121179048 578 False 455.000000 455 81.100000 1138 1710 1 chr1B.!!$F1 572
13 TraesCS4A01G288400 chr1D 77650298 77650900 602 False 446.000000 446 80.298000 1138 1731 1 chr1D.!!$F1 593

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
629 1707 0.247736 CGAGACAAGTTGAGGGGGAG 59.752 60.0 10.54 0.0 0.00 4.30 F
651 1744 0.441145 GGGTTCGGTGAATCGTTTCG 59.559 55.0 2.00 0.0 34.39 3.46 F
832 5045 0.465824 TCCTCTACGGCTAGGAGCAC 60.466 60.0 0.21 0.0 44.75 4.40 F
2831 8294 0.467290 GAACAAGCCACCACCAAGGA 60.467 55.0 0.00 0.0 41.22 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 7011 0.178876 TGGTGGGGATGAAGACCAGA 60.179 55.000 0.00 0.0 33.44 3.86 R
2172 7611 2.126071 AGGTTGTCGATCGCCGTG 60.126 61.111 11.09 0.0 39.75 4.94 R
2834 8297 2.125512 CGCTGGGACTGGTGCTAC 60.126 66.667 0.00 0.0 0.00 3.58 R
3694 10835 0.249953 TCTTGGAGGTTTGCGCGTTA 60.250 50.000 8.43 0.0 0.00 3.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 6.296432 GGCCCTCATATGATGATGTAAACCTA 60.296 42.308 5.72 0.00 38.85 3.08
140 145 2.097466 CGATAGAGTTTTGGGCGCAATT 59.903 45.455 17.68 6.22 39.76 2.32
149 154 1.249469 TGGGCGCAATTGCATCTTGA 61.249 50.000 28.77 5.58 42.21 3.02
187 203 3.398318 TGGGGTAGCATCTCTTCTACA 57.602 47.619 0.00 0.00 37.49 2.74
355 1196 1.455248 CTAAAATTTCACGGGCGGGA 58.545 50.000 0.00 0.00 0.00 5.14
416 1257 3.349022 TGATTCAATCCGTAAACACCCC 58.651 45.455 0.00 0.00 0.00 4.95
466 1500 0.809636 TGGCATGCCGATACAAGTCG 60.810 55.000 30.87 0.00 41.13 4.18
492 1526 4.993905 TCGTAGTACACATGTCATCTTGG 58.006 43.478 0.00 0.00 0.00 3.61
500 1534 4.946157 ACACATGTCATCTTGGGAGAATTC 59.054 41.667 0.00 0.00 35.07 2.17
501 1535 4.945543 CACATGTCATCTTGGGAGAATTCA 59.054 41.667 8.44 0.00 35.07 2.57
532 1566 9.364989 TGAAAATTATGAAATGGTTTCGATTCC 57.635 29.630 0.00 0.00 42.55 3.01
538 1572 5.953183 TGAAATGGTTTCGATTCCTCATTG 58.047 37.500 7.69 0.00 42.55 2.82
613 1691 1.070309 GCTGTGCTCAAAGTTCACGAG 60.070 52.381 0.00 0.00 33.69 4.18
614 1692 2.473816 CTGTGCTCAAAGTTCACGAGA 58.526 47.619 0.00 0.00 33.69 4.04
628 1706 0.471211 ACGAGACAAGTTGAGGGGGA 60.471 55.000 10.54 0.00 0.00 4.81
629 1707 0.247736 CGAGACAAGTTGAGGGGGAG 59.752 60.000 10.54 0.00 0.00 4.30
631 1709 0.842467 AGACAAGTTGAGGGGGAGGG 60.842 60.000 10.54 0.00 0.00 4.30
632 1710 1.852626 ACAAGTTGAGGGGGAGGGG 60.853 63.158 10.54 0.00 0.00 4.79
633 1711 2.204306 AAGTTGAGGGGGAGGGGG 60.204 66.667 0.00 0.00 0.00 5.40
649 1742 0.607217 GGGGGTTCGGTGAATCGTTT 60.607 55.000 0.00 0.00 0.00 3.60
651 1744 0.441145 GGGTTCGGTGAATCGTTTCG 59.559 55.000 2.00 0.00 34.39 3.46
695 1788 5.985175 TCATCAAAGGGGGTTGATACATA 57.015 39.130 0.37 0.00 44.58 2.29
707 1800 5.590259 GGGTTGATACATATGTGCAAGAGTT 59.410 40.000 18.81 0.00 0.00 3.01
709 1802 7.254795 GGGTTGATACATATGTGCAAGAGTTAC 60.255 40.741 18.81 9.57 0.00 2.50
732 1825 5.175127 CCCAACCAATTAACATTGCCTTAC 58.825 41.667 0.00 0.00 38.88 2.34
784 1877 2.008752 TCGCATGTCCGCCATATATG 57.991 50.000 5.68 5.68 30.71 1.78
827 1920 0.885196 GCATCTCCTCTACGGCTAGG 59.115 60.000 0.00 0.00 0.00 3.02
831 5044 1.920532 TCCTCTACGGCTAGGAGCA 59.079 57.895 0.21 0.00 44.75 4.26
832 5045 0.465824 TCCTCTACGGCTAGGAGCAC 60.466 60.000 0.21 0.00 44.75 4.40
846 5059 5.643777 GCTAGGAGCACTTTTCTTATCACAA 59.356 40.000 0.00 0.00 41.89 3.33
906 5119 4.331168 CGTGAGAGAATTGAGGATGGAAAC 59.669 45.833 0.00 0.00 0.00 2.78
907 5120 4.331168 GTGAGAGAATTGAGGATGGAAACG 59.669 45.833 0.00 0.00 0.00 3.60
908 5121 4.222810 TGAGAGAATTGAGGATGGAAACGA 59.777 41.667 0.00 0.00 0.00 3.85
909 5122 5.104776 TGAGAGAATTGAGGATGGAAACGAT 60.105 40.000 0.00 0.00 0.00 3.73
932 6220 6.768029 TTCCATTTGATTTTTCTTTGCTCG 57.232 33.333 0.00 0.00 0.00 5.03
942 6230 2.031258 TCTTTGCTCGTGTGGTCAAA 57.969 45.000 0.00 0.00 0.00 2.69
957 6245 4.702131 GTGGTCAAAATAGGAAGCTGACAT 59.298 41.667 0.00 0.00 38.50 3.06
958 6246 5.880332 GTGGTCAAAATAGGAAGCTGACATA 59.120 40.000 0.00 0.00 38.50 2.29
959 6247 6.543831 GTGGTCAAAATAGGAAGCTGACATAT 59.456 38.462 0.00 0.00 38.50 1.78
963 6251 6.925718 TCAAAATAGGAAGCTGACATATCTCG 59.074 38.462 0.00 0.00 0.00 4.04
987 6275 1.865655 GCTGATCATTCTCGCGCTACA 60.866 52.381 5.56 0.00 0.00 2.74
988 6276 2.670479 CTGATCATTCTCGCGCTACAT 58.330 47.619 5.56 0.00 0.00 2.29
989 6277 3.826466 CTGATCATTCTCGCGCTACATA 58.174 45.455 5.56 0.00 0.00 2.29
990 6278 4.419280 CTGATCATTCTCGCGCTACATAT 58.581 43.478 5.56 0.00 0.00 1.78
991 6279 4.415735 TGATCATTCTCGCGCTACATATC 58.584 43.478 5.56 1.17 0.00 1.63
992 6280 4.156739 TGATCATTCTCGCGCTACATATCT 59.843 41.667 5.56 0.00 0.00 1.98
993 6281 4.084889 TCATTCTCGCGCTACATATCTC 57.915 45.455 5.56 0.00 0.00 2.75
994 6282 3.502211 TCATTCTCGCGCTACATATCTCA 59.498 43.478 5.56 0.00 0.00 3.27
995 6283 4.156739 TCATTCTCGCGCTACATATCTCAT 59.843 41.667 5.56 0.00 0.00 2.90
996 6284 5.354234 TCATTCTCGCGCTACATATCTCATA 59.646 40.000 5.56 0.00 0.00 2.15
997 6285 5.819825 TTCTCGCGCTACATATCTCATAT 57.180 39.130 5.56 0.00 0.00 1.78
998 6286 6.920569 TTCTCGCGCTACATATCTCATATA 57.079 37.500 5.56 0.00 0.00 0.86
999 6287 7.497925 TTCTCGCGCTACATATCTCATATAT 57.502 36.000 5.56 0.00 0.00 0.86
1849 7204 1.761174 GTGCTCAAGTTCCCCAGGA 59.239 57.895 0.00 0.00 0.00 3.86
1965 7326 4.039092 CTGCCCACCCAGTCCCAG 62.039 72.222 0.00 0.00 0.00 4.45
1968 7329 3.330720 CCCACCCAGTCCCAGTCC 61.331 72.222 0.00 0.00 0.00 3.85
1975 7336 1.261238 CCAGTCCCAGTCCCAGTCTC 61.261 65.000 0.00 0.00 0.00 3.36
2567 8006 1.011968 TACATCCTCAACGTGCGCAC 61.012 55.000 30.42 30.42 0.00 5.34
2831 8294 0.467290 GAACAAGCCACCACCAAGGA 60.467 55.000 0.00 0.00 41.22 3.36
2872 8350 3.592856 AACGCCGTCGCCACCAATA 62.593 57.895 0.00 0.00 39.84 1.90
2873 8351 2.816083 CGCCGTCGCCACCAATAA 60.816 61.111 0.00 0.00 0.00 1.40
2874 8352 2.177580 CGCCGTCGCCACCAATAAT 61.178 57.895 0.00 0.00 0.00 1.28
2940 8462 3.057969 TCCATGGAATCATACGGATGC 57.942 47.619 13.46 0.00 36.02 3.91
2944 8466 3.490439 TGGAATCATACGGATGCATGT 57.510 42.857 2.46 0.00 36.02 3.21
2979 8503 6.420604 ACATGCTTTGCTTAATTTGTGTGTAC 59.579 34.615 0.00 0.00 0.00 2.90
2981 8505 5.976534 TGCTTTGCTTAATTTGTGTGTACAG 59.023 36.000 0.00 0.00 38.23 2.74
2982 8506 5.402270 GCTTTGCTTAATTTGTGTGTACAGG 59.598 40.000 0.00 0.00 38.23 4.00
3021 8549 9.911138 TCGATTGTATAGTTGTACTACAAAACA 57.089 29.630 10.09 7.29 40.15 2.83
3039 9388 6.865205 ACAAAACAGATAGCTGAAATTCTTGC 59.135 34.615 16.32 0.00 45.17 4.01
3050 9399 6.593382 AGCTGAAATTCTTGCTTCAGTAGTAG 59.407 38.462 12.09 0.00 46.76 2.57
3053 9402 8.758633 TGAAATTCTTGCTTCAGTAGTAGTAC 57.241 34.615 0.00 0.00 0.00 2.73
3071 9420 0.602905 ACACAAGTAGCGGGTGAAGC 60.603 55.000 0.00 0.00 36.42 3.86
3102 9451 2.127271 TGTGTGATCCCGCATTTCAT 57.873 45.000 0.00 0.00 35.00 2.57
3122 9471 3.825908 TGGAAAGGGGACTGCTTTAAT 57.174 42.857 0.00 0.00 42.68 1.40
3125 9474 4.526650 TGGAAAGGGGACTGCTTTAATTTC 59.473 41.667 0.00 0.00 42.68 2.17
3127 9476 5.187772 GGAAAGGGGACTGCTTTAATTTCAT 59.812 40.000 0.00 0.00 42.68 2.57
3130 9479 6.041423 AGGGGACTGCTTTAATTTCATTTG 57.959 37.500 0.00 0.00 41.13 2.32
3140 9492 7.276218 TGCTTTAATTTCATTTGCTAGATGTGC 59.724 33.333 0.00 0.00 0.00 4.57
3172 9524 3.003897 TGATTGTTCCAACGGTAGTTTGC 59.996 43.478 0.00 0.00 38.79 3.68
3175 10316 1.265905 GTTCCAACGGTAGTTTGCTGG 59.734 52.381 0.00 0.00 38.79 4.85
3197 10338 4.393062 GGATCGTCATGTGAATGAAACAGT 59.607 41.667 0.00 0.00 31.60 3.55
3198 10339 4.730600 TCGTCATGTGAATGAAACAGTG 57.269 40.909 0.00 0.00 31.60 3.66
3203 10344 5.400485 GTCATGTGAATGAAACAGTGAAAGC 59.600 40.000 0.00 0.00 31.60 3.51
3205 10346 5.173774 TGTGAATGAAACAGTGAAAGCTC 57.826 39.130 0.00 0.00 0.00 4.09
3207 10348 5.125257 TGTGAATGAAACAGTGAAAGCTCAA 59.875 36.000 0.00 0.00 31.88 3.02
3208 10349 5.456822 GTGAATGAAACAGTGAAAGCTCAAC 59.543 40.000 0.00 0.00 31.88 3.18
3210 10351 2.354510 TGAAACAGTGAAAGCTCAACGG 59.645 45.455 0.00 0.00 31.88 4.44
3215 10356 2.614057 CAGTGAAAGCTCAACGGAAACT 59.386 45.455 0.00 0.00 31.88 2.66
3225 10366 5.022021 GCTCAACGGAAACTATCAAAATCG 58.978 41.667 0.00 0.00 0.00 3.34
3229 10370 6.311935 TCAACGGAAACTATCAAAATCGTAGG 59.688 38.462 0.00 0.00 0.00 3.18
3230 10371 5.114081 ACGGAAACTATCAAAATCGTAGGG 58.886 41.667 0.00 0.00 0.00 3.53
3232 10373 4.879545 GGAAACTATCAAAATCGTAGGGCA 59.120 41.667 0.00 0.00 0.00 5.36
3233 10374 5.531287 GGAAACTATCAAAATCGTAGGGCAT 59.469 40.000 0.00 0.00 0.00 4.40
3240 10381 2.550830 AATCGTAGGGCATCATCACC 57.449 50.000 0.00 0.00 0.00 4.02
3241 10382 0.318441 ATCGTAGGGCATCATCACCG 59.682 55.000 0.00 0.00 0.00 4.94
3247 10388 1.596477 GGCATCATCACCGAGCCTC 60.596 63.158 0.00 0.00 42.01 4.70
3267 10408 4.614673 CAACAAGCCTCGTGTTGC 57.385 55.556 11.37 0.00 46.63 4.17
3285 10426 3.258290 GCTCGGCGCTCTTAGCAC 61.258 66.667 7.64 0.00 42.58 4.40
3286 10427 2.951745 CTCGGCGCTCTTAGCACG 60.952 66.667 7.64 0.00 42.58 5.34
3287 10428 3.396911 CTCGGCGCTCTTAGCACGA 62.397 63.158 7.64 12.89 44.21 4.35
3288 10429 2.951745 CGGCGCTCTTAGCACGAG 60.952 66.667 7.64 0.00 42.58 4.18
3289 10430 2.182030 GGCGCTCTTAGCACGAGT 59.818 61.111 7.64 0.00 42.58 4.18
3295 10436 2.255316 GCTCTTAGCACGAGTCTTGTC 58.745 52.381 0.00 0.00 41.89 3.18
3302 10443 0.109086 CACGAGTCTTGTCGCATCCT 60.109 55.000 0.00 0.00 44.06 3.24
3304 10445 0.863538 CGAGTCTTGTCGCATCCTCG 60.864 60.000 0.00 0.00 36.31 4.63
3305 10446 0.526524 GAGTCTTGTCGCATCCTCGG 60.527 60.000 0.00 0.00 0.00 4.63
3307 10448 0.103208 GTCTTGTCGCATCCTCGGAT 59.897 55.000 0.00 0.00 34.81 4.18
3313 10454 2.167693 TGTCGCATCCTCGGATAGTTTT 59.832 45.455 0.00 0.00 32.93 2.43
3314 10455 3.382227 TGTCGCATCCTCGGATAGTTTTA 59.618 43.478 0.00 0.00 32.93 1.52
3316 10457 4.621886 GTCGCATCCTCGGATAGTTTTATC 59.378 45.833 0.00 0.00 35.87 1.75
3318 10459 4.615223 CGCATCCTCGGATAGTTTTATCGA 60.615 45.833 0.00 0.00 37.20 3.59
3320 10461 6.561614 GCATCCTCGGATAGTTTTATCGATA 58.438 40.000 0.00 0.00 37.20 2.92
3322 10463 7.380065 GCATCCTCGGATAGTTTTATCGATATC 59.620 40.741 5.84 0.40 37.20 1.63
3334 10475 8.064222 AGTTTTATCGATATCTTTTCATGTGCG 58.936 33.333 5.84 0.00 0.00 5.34
3363 10504 2.674357 ACGTAGTTTGTGTTGCTTTCGT 59.326 40.909 0.00 0.00 37.78 3.85
3385 10526 2.225491 GCGTCTTGCAACAAAGGTCATA 59.775 45.455 0.00 0.00 45.45 2.15
3389 10530 4.622740 GTCTTGCAACAAAGGTCATATTGC 59.377 41.667 0.00 0.00 44.66 3.56
3393 10534 5.002464 GCAACAAAGGTCATATTGCAGAT 57.998 39.130 2.54 0.00 44.01 2.90
3395 10536 5.393352 GCAACAAAGGTCATATTGCAGATGA 60.393 40.000 8.82 8.82 44.01 2.92
3406 10547 2.680312 TGCAGATGACTTAGTCAGGC 57.320 50.000 20.12 20.89 46.04 4.85
3408 10549 2.275318 GCAGATGACTTAGTCAGGCAC 58.725 52.381 20.12 11.20 46.55 5.01
3409 10550 2.354103 GCAGATGACTTAGTCAGGCACA 60.354 50.000 20.12 0.00 46.55 4.57
3410 10551 3.681034 GCAGATGACTTAGTCAGGCACAT 60.681 47.826 20.12 2.37 46.55 3.21
3411 10552 3.869832 CAGATGACTTAGTCAGGCACATG 59.130 47.826 20.12 8.54 46.55 3.21
3413 10554 1.339055 TGACTTAGTCAGGCACATGGC 60.339 52.381 11.42 0.00 34.47 4.40
3414 10555 0.391661 ACTTAGTCAGGCACATGGCG 60.392 55.000 0.00 0.00 46.16 5.69
3415 10556 1.709147 CTTAGTCAGGCACATGGCGC 61.709 60.000 0.00 0.00 46.16 6.53
3416 10557 2.462125 TTAGTCAGGCACATGGCGCA 62.462 55.000 10.83 0.00 46.16 6.09
3417 10558 2.256072 TAGTCAGGCACATGGCGCAT 62.256 55.000 10.83 0.00 46.16 4.73
3418 10559 1.819208 GTCAGGCACATGGCGCATA 60.819 57.895 10.83 0.00 46.16 3.14
3419 10560 1.524393 TCAGGCACATGGCGCATAG 60.524 57.895 10.83 0.00 46.16 2.23
3420 10561 1.524393 CAGGCACATGGCGCATAGA 60.524 57.895 10.83 0.00 46.16 1.98
3421 10562 1.227764 AGGCACATGGCGCATAGAG 60.228 57.895 10.83 0.00 46.16 2.43
3422 10563 2.256591 GGCACATGGCGCATAGAGG 61.257 63.158 10.83 0.00 46.16 3.69
3425 10566 0.035881 CACATGGCGCATAGAGGGAT 59.964 55.000 10.83 0.00 0.00 3.85
3439 10580 7.756395 CATAGAGGGATGCATCTAAAAACAT 57.244 36.000 25.28 5.96 32.05 2.71
3440 10581 8.174733 CATAGAGGGATGCATCTAAAAACATT 57.825 34.615 25.28 5.61 32.05 2.71
3441 10582 8.636213 CATAGAGGGATGCATCTAAAAACATTT 58.364 33.333 25.28 4.25 32.05 2.32
3442 10583 7.486407 AGAGGGATGCATCTAAAAACATTTT 57.514 32.000 25.28 0.00 0.00 1.82
3443 10584 7.325694 AGAGGGATGCATCTAAAAACATTTTG 58.674 34.615 25.28 0.00 0.00 2.44
3446 10587 6.372381 GGGATGCATCTAAAAACATTTTGCTT 59.628 34.615 25.28 0.00 0.00 3.91
3447 10588 7.094677 GGGATGCATCTAAAAACATTTTGCTTT 60.095 33.333 25.28 0.00 0.00 3.51
3448 10589 7.959109 GGATGCATCTAAAAACATTTTGCTTTC 59.041 33.333 25.28 0.00 0.00 2.62
3452 10593 7.894753 GCATCTAAAAACATTTTGCTTTCGATC 59.105 33.333 0.00 0.00 0.00 3.69
3453 10594 9.132521 CATCTAAAAACATTTTGCTTTCGATCT 57.867 29.630 0.00 0.00 0.00 2.75
3457 10598 2.420022 ACATTTTGCTTTCGATCTCCCG 59.580 45.455 0.00 0.00 0.00 5.14
3461 10602 0.391130 TGCTTTCGATCTCCCGGTTG 60.391 55.000 0.00 0.00 0.00 3.77
3462 10603 0.108329 GCTTTCGATCTCCCGGTTGA 60.108 55.000 0.00 0.00 0.00 3.18
3463 10604 1.641577 CTTTCGATCTCCCGGTTGAC 58.358 55.000 0.00 0.00 0.00 3.18
3465 10606 2.552585 TTCGATCTCCCGGTTGACGC 62.553 60.000 0.00 0.00 42.52 5.19
3469 10610 2.558554 ATCTCCCGGTTGACGCGAAG 62.559 60.000 15.93 0.00 42.52 3.79
3489 10630 6.620006 CGAAGCGTTTTCGTTTTAATTTTCA 58.380 32.000 13.64 0.00 45.82 2.69
3491 10632 7.785665 CGAAGCGTTTTCGTTTTAATTTTCAAT 59.214 29.630 13.64 0.00 45.82 2.57
3493 10634 9.762062 AAGCGTTTTCGTTTTAATTTTCAATTT 57.238 22.222 0.00 0.00 43.61 1.82
3494 10635 9.762062 AGCGTTTTCGTTTTAATTTTCAATTTT 57.238 22.222 0.00 0.00 46.03 1.82
3512 10653 8.810652 TCAATTTTATTTTGCAACTGTCTACC 57.189 30.769 0.00 0.00 0.00 3.18
3513 10654 8.417106 TCAATTTTATTTTGCAACTGTCTACCA 58.583 29.630 0.00 0.00 0.00 3.25
3515 10656 8.761575 ATTTTATTTTGCAACTGTCTACCATG 57.238 30.769 0.00 0.00 0.00 3.66
3516 10657 7.517614 TTTATTTTGCAACTGTCTACCATGA 57.482 32.000 0.00 0.00 0.00 3.07
3521 10662 5.627499 TGCAACTGTCTACCATGATTTTC 57.373 39.130 0.00 0.00 0.00 2.29
3546 10687 9.023962 TCTGCAAAAGAACAAATTATCCAGTAT 57.976 29.630 0.00 0.00 29.54 2.12
3579 10720 4.365899 TGTACATGACATGACGTAGGAC 57.634 45.455 22.19 0.00 31.20 3.85
3580 10721 3.181504 TGTACATGACATGACGTAGGACG 60.182 47.826 22.19 0.00 39.54 4.79
3582 10723 2.490509 ACATGACATGACGTAGGACGAA 59.509 45.455 22.19 0.00 46.05 3.85
3583 10724 2.913777 TGACATGACGTAGGACGAAG 57.086 50.000 5.94 0.00 46.05 3.79
3585 10726 3.014623 TGACATGACGTAGGACGAAGAT 58.985 45.455 5.94 0.00 46.05 2.40
3586 10727 4.193865 TGACATGACGTAGGACGAAGATA 58.806 43.478 5.94 0.00 46.05 1.98
3587 10728 4.637091 TGACATGACGTAGGACGAAGATAA 59.363 41.667 5.94 0.00 46.05 1.75
3588 10729 5.298527 TGACATGACGTAGGACGAAGATAAT 59.701 40.000 5.94 0.00 46.05 1.28
3589 10730 6.484308 TGACATGACGTAGGACGAAGATAATA 59.516 38.462 5.94 0.00 46.05 0.98
3590 10731 6.900189 ACATGACGTAGGACGAAGATAATAG 58.100 40.000 5.94 0.00 46.05 1.73
3592 10733 7.228108 ACATGACGTAGGACGAAGATAATAGAA 59.772 37.037 5.94 0.00 46.05 2.10
3594 10735 7.988737 TGACGTAGGACGAAGATAATAGAAAA 58.011 34.615 5.94 0.00 46.05 2.29
3595 10736 8.127327 TGACGTAGGACGAAGATAATAGAAAAG 58.873 37.037 5.94 0.00 46.05 2.27
3596 10737 7.994194 ACGTAGGACGAAGATAATAGAAAAGT 58.006 34.615 5.94 0.00 46.05 2.66
3597 10738 8.127954 ACGTAGGACGAAGATAATAGAAAAGTC 58.872 37.037 5.94 0.00 46.05 3.01
3598 10739 8.344098 CGTAGGACGAAGATAATAGAAAAGTCT 58.656 37.037 0.00 0.00 46.05 3.24
3611 10752 7.982371 ATAGAAAAGTCTTATAACGTCACCG 57.018 36.000 0.00 0.00 36.26 4.94
3612 10753 6.017400 AGAAAAGTCTTATAACGTCACCGA 57.983 37.500 0.00 0.00 37.88 4.69
3613 10754 5.860716 AGAAAAGTCTTATAACGTCACCGAC 59.139 40.000 0.00 0.00 37.88 4.79
3614 10755 3.772060 AGTCTTATAACGTCACCGACC 57.228 47.619 0.00 0.00 37.88 4.79
3624 10765 1.871039 CGTCACCGACCAAATCTTGTT 59.129 47.619 0.00 0.00 35.63 2.83
3644 10785 6.426980 TGTTGCAATCTGATCAGTTACATC 57.573 37.500 21.92 14.28 0.00 3.06
3650 10791 6.763135 GCAATCTGATCAGTTACATCTTACCA 59.237 38.462 21.92 0.00 0.00 3.25
3652 10793 7.667575 ATCTGATCAGTTACATCTTACCAGT 57.332 36.000 21.92 0.00 0.00 4.00
3653 10794 6.867550 TCTGATCAGTTACATCTTACCAGTG 58.132 40.000 21.92 0.00 0.00 3.66
3654 10795 5.419542 TGATCAGTTACATCTTACCAGTGC 58.580 41.667 0.00 0.00 0.00 4.40
3655 10796 4.882842 TCAGTTACATCTTACCAGTGCA 57.117 40.909 0.00 0.00 0.00 4.57
3656 10797 5.420725 TCAGTTACATCTTACCAGTGCAT 57.579 39.130 0.00 0.00 0.00 3.96
3657 10798 5.178061 TCAGTTACATCTTACCAGTGCATG 58.822 41.667 0.00 0.00 0.00 4.06
3658 10799 4.937620 CAGTTACATCTTACCAGTGCATGT 59.062 41.667 0.00 0.00 0.00 3.21
3659 10800 5.063944 CAGTTACATCTTACCAGTGCATGTC 59.936 44.000 0.00 0.00 0.00 3.06
3660 10801 3.988976 ACATCTTACCAGTGCATGTCT 57.011 42.857 0.00 0.00 0.00 3.41
3661 10802 6.154534 AGTTACATCTTACCAGTGCATGTCTA 59.845 38.462 0.00 0.00 0.00 2.59
3662 10803 5.620738 ACATCTTACCAGTGCATGTCTAT 57.379 39.130 0.00 0.00 0.00 1.98
3663 10804 5.994250 ACATCTTACCAGTGCATGTCTATT 58.006 37.500 0.00 0.00 0.00 1.73
3688 10829 2.967599 TCTAATCACGTGCATGCTCT 57.032 45.000 20.33 1.35 0.00 4.09
3692 10833 2.896745 ATCACGTGCATGCTCTCATA 57.103 45.000 20.33 0.31 0.00 2.15
3693 10834 2.896745 TCACGTGCATGCTCTCATAT 57.103 45.000 20.33 0.00 0.00 1.78
3694 10835 3.183793 TCACGTGCATGCTCTCATATT 57.816 42.857 20.33 0.00 0.00 1.28
3695 10836 4.320608 TCACGTGCATGCTCTCATATTA 57.679 40.909 20.33 0.00 0.00 0.98
3697 10838 4.507756 TCACGTGCATGCTCTCATATTAAC 59.492 41.667 20.33 3.26 0.00 2.01
3698 10839 3.490896 ACGTGCATGCTCTCATATTAACG 59.509 43.478 20.33 17.49 33.41 3.18
3736 10877 4.707105 TCCGTGTGATCAATATTGCTGAT 58.293 39.130 10.76 0.00 36.21 2.90
3741 10882 7.286508 CGTGTGATCAATATTGCTGATTAGTC 58.713 38.462 10.76 0.34 33.63 2.59
3742 10883 7.570140 CGTGTGATCAATATTGCTGATTAGTCC 60.570 40.741 10.76 0.00 33.63 3.85
3743 10884 7.227314 GTGTGATCAATATTGCTGATTAGTCCA 59.773 37.037 10.76 0.00 33.63 4.02
3745 10886 8.449397 GTGATCAATATTGCTGATTAGTCCATC 58.551 37.037 10.76 4.81 33.63 3.51
3746 10887 8.158789 TGATCAATATTGCTGATTAGTCCATCA 58.841 33.333 10.76 7.16 33.63 3.07
3767 10932 5.924356 TCATGACACTTGTTAGAAGTTCCA 58.076 37.500 0.00 0.00 0.00 3.53
3770 10935 5.601662 TGACACTTGTTAGAAGTTCCAGAG 58.398 41.667 0.00 0.00 0.00 3.35
3771 10936 4.962155 ACACTTGTTAGAAGTTCCAGAGG 58.038 43.478 0.00 0.00 0.00 3.69
3798 10963 1.210478 GAGAGCTACCCATTTCTGGCA 59.790 52.381 0.00 0.00 41.64 4.92
3882 11047 7.273320 TCTTGAGTTACTGAATATACTCCGG 57.727 40.000 0.00 0.00 36.94 5.14
3903 11068 1.323271 CGAGAGCAGCTTGGTAGGGA 61.323 60.000 0.00 0.00 0.00 4.20
3904 11069 1.127343 GAGAGCAGCTTGGTAGGGAT 58.873 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 145 3.564053 TGCAGATATGGTCAAGATGCA 57.436 42.857 0.00 0.00 39.67 3.96
149 154 3.626475 CCCCATATGCATGCAGATATGGT 60.626 47.826 36.08 20.78 42.62 3.55
187 203 8.637196 AGAAAAAGGCTAAAGTGCTACTAAAT 57.363 30.769 0.00 0.00 0.00 1.40
355 1196 4.228824 TGAGTGTTAGTTAGGGAAGTGGT 58.771 43.478 0.00 0.00 0.00 4.16
447 1481 0.809636 CGACTTGTATCGGCATGCCA 60.810 55.000 34.93 22.41 38.47 4.92
455 1489 4.768659 ACTACGAGTACGACTTGTATCG 57.231 45.455 12.57 0.00 42.47 2.92
489 1523 7.499200 AATTTTCATCCATGAATTCTCCCAA 57.501 32.000 7.05 0.00 45.30 4.12
501 1535 9.316730 CGAAACCATTTCATAATTTTCATCCAT 57.683 29.630 2.50 0.00 39.63 3.41
532 1566 6.927381 ACTTGAGCAAAGAAAAATCCAATGAG 59.073 34.615 6.20 0.00 39.38 2.90
538 1572 5.173854 CGTCAACTTGAGCAAAGAAAAATCC 59.826 40.000 6.20 0.00 39.38 3.01
613 1691 1.685820 CCCTCCCCCTCAACTTGTC 59.314 63.158 0.00 0.00 0.00 3.18
614 1692 1.852626 CCCCTCCCCCTCAACTTGT 60.853 63.158 0.00 0.00 0.00 3.16
631 1709 0.800631 GAAACGATTCACCGAACCCC 59.199 55.000 0.00 0.00 35.54 4.95
632 1710 0.441145 CGAAACGATTCACCGAACCC 59.559 55.000 6.23 0.00 35.15 4.11
633 1711 1.142474 ACGAAACGATTCACCGAACC 58.858 50.000 6.23 0.00 35.15 3.62
634 1712 2.556806 CAACGAAACGATTCACCGAAC 58.443 47.619 6.23 0.00 35.15 3.95
635 1713 1.070443 GCAACGAAACGATTCACCGAA 60.070 47.619 6.23 0.00 35.15 4.30
636 1714 0.509499 GCAACGAAACGATTCACCGA 59.491 50.000 6.23 0.00 35.15 4.69
695 1788 2.158534 TGGTTGGGTAACTCTTGCACAT 60.159 45.455 0.00 0.00 36.99 3.21
707 1800 4.421131 AGGCAATGTTAATTGGTTGGGTA 58.579 39.130 1.01 0.00 42.98 3.69
709 1802 3.979101 AGGCAATGTTAATTGGTTGGG 57.021 42.857 1.01 0.00 42.98 4.12
746 1839 1.810151 GATTGCGCCCAAAACTCTACA 59.190 47.619 4.18 0.00 34.05 2.74
784 1877 5.440234 ACCCGATCGATATATATGCAGAC 57.560 43.478 18.66 0.00 0.00 3.51
801 1894 1.542767 CGTAGAGGAGATGCTACCCGA 60.543 57.143 0.00 0.00 34.84 5.14
802 1895 0.875728 CGTAGAGGAGATGCTACCCG 59.124 60.000 0.00 0.00 34.84 5.28
803 1896 1.249407 CCGTAGAGGAGATGCTACCC 58.751 60.000 0.00 0.00 45.00 3.69
804 1897 0.599060 GCCGTAGAGGAGATGCTACC 59.401 60.000 0.00 0.00 45.00 3.18
827 1920 7.369803 TCATCTTGTGATAAGAAAAGTGCTC 57.630 36.000 0.00 0.00 0.00 4.26
846 5059 7.726216 TGTACGAACAGGATTTATCATCATCT 58.274 34.615 0.00 0.00 0.00 2.90
863 5076 2.473868 CGATGGCATGTGTTGTACGAAC 60.474 50.000 3.81 0.00 0.00 3.95
864 5077 1.729517 CGATGGCATGTGTTGTACGAA 59.270 47.619 3.81 0.00 0.00 3.85
906 5119 7.355332 AGCAAAGAAAAATCAAATGGAATCG 57.645 32.000 0.00 0.00 0.00 3.34
907 5120 7.116805 ACGAGCAAAGAAAAATCAAATGGAATC 59.883 33.333 0.00 0.00 0.00 2.52
908 5121 6.930722 ACGAGCAAAGAAAAATCAAATGGAAT 59.069 30.769 0.00 0.00 0.00 3.01
909 5122 6.200665 CACGAGCAAAGAAAAATCAAATGGAA 59.799 34.615 0.00 0.00 0.00 3.53
932 6220 4.072131 TCAGCTTCCTATTTTGACCACAC 58.928 43.478 0.00 0.00 0.00 3.82
942 6230 4.526262 AGCGAGATATGTCAGCTTCCTATT 59.474 41.667 11.52 0.00 37.33 1.73
957 6245 4.554292 GAGAATGATCAGCAAGCGAGATA 58.446 43.478 0.09 0.00 0.00 1.98
958 6246 3.391965 GAGAATGATCAGCAAGCGAGAT 58.608 45.455 0.09 3.35 0.00 2.75
959 6247 2.797439 CGAGAATGATCAGCAAGCGAGA 60.797 50.000 0.09 0.00 0.00 4.04
963 6251 0.042361 CGCGAGAATGATCAGCAAGC 60.042 55.000 0.00 2.38 33.01 4.01
1269 6588 2.812358 TGAAGAAGCTGAGCGTGTTA 57.188 45.000 2.38 0.00 0.00 2.41
1680 7011 0.178876 TGGTGGGGATGAAGACCAGA 60.179 55.000 0.00 0.00 33.44 3.86
1965 7326 3.605895 GGGACGAGAGACTGGGAC 58.394 66.667 0.00 0.00 0.00 4.46
2172 7611 2.126071 AGGTTGTCGATCGCCGTG 60.126 61.111 11.09 0.00 39.75 4.94
2834 8297 2.125512 CGCTGGGACTGGTGCTAC 60.126 66.667 0.00 0.00 0.00 3.58
2836 8299 4.008933 GTCGCTGGGACTGGTGCT 62.009 66.667 16.61 0.00 42.62 4.40
2837 8300 3.825160 TTGTCGCTGGGACTGGTGC 62.825 63.158 22.89 0.00 46.24 5.01
2872 8350 1.098050 GAACCGATCTTGCTGCCATT 58.902 50.000 0.00 0.00 0.00 3.16
2873 8351 0.035152 TGAACCGATCTTGCTGCCAT 60.035 50.000 0.00 0.00 0.00 4.40
2874 8352 0.674581 CTGAACCGATCTTGCTGCCA 60.675 55.000 0.00 0.00 0.00 4.92
2944 8466 2.821378 AGCAAAGCATGTGTAGCATTCA 59.179 40.909 0.00 0.00 35.19 2.57
3021 8549 6.680874 CTGAAGCAAGAATTTCAGCTATCT 57.319 37.500 14.25 2.69 42.48 1.98
3039 9388 6.249359 CGCTACTTGTGTACTACTACTGAAG 58.751 44.000 0.00 0.00 0.00 3.02
3050 9399 2.334838 CTTCACCCGCTACTTGTGTAC 58.665 52.381 0.00 0.00 0.00 2.90
3053 9402 0.320771 AGCTTCACCCGCTACTTGTG 60.321 55.000 0.00 0.00 35.63 3.33
3071 9420 2.740981 GGATCACACAAGACTTGCTGAG 59.259 50.000 15.24 10.84 0.00 3.35
3102 9451 3.825908 ATTAAAGCAGTCCCCTTTCCA 57.174 42.857 0.00 0.00 34.58 3.53
3122 9471 4.081406 ACCTGCACATCTAGCAAATGAAA 58.919 39.130 0.00 0.00 42.17 2.69
3125 9474 4.877823 TCTAACCTGCACATCTAGCAAATG 59.122 41.667 0.00 0.00 42.17 2.32
3127 9476 4.551702 TCTAACCTGCACATCTAGCAAA 57.448 40.909 0.00 0.00 42.17 3.68
3130 9479 4.697514 TCAATCTAACCTGCACATCTAGC 58.302 43.478 0.00 0.00 0.00 3.42
3172 9524 4.392754 TGTTTCATTCACATGACGATCCAG 59.607 41.667 0.00 0.00 39.28 3.86
3175 10316 5.120674 TCACTGTTTCATTCACATGACGATC 59.879 40.000 0.00 0.00 39.28 3.69
3197 10338 4.637276 TGATAGTTTCCGTTGAGCTTTCA 58.363 39.130 0.00 0.00 0.00 2.69
3198 10339 5.607119 TTGATAGTTTCCGTTGAGCTTTC 57.393 39.130 0.00 0.00 0.00 2.62
3203 10344 6.165659 ACGATTTTGATAGTTTCCGTTGAG 57.834 37.500 0.00 0.00 0.00 3.02
3205 10346 6.456449 CCCTACGATTTTGATAGTTTCCGTTG 60.456 42.308 0.00 0.00 0.00 4.10
3207 10348 5.114081 CCCTACGATTTTGATAGTTTCCGT 58.886 41.667 0.00 0.00 0.00 4.69
3208 10349 4.025145 GCCCTACGATTTTGATAGTTTCCG 60.025 45.833 0.00 0.00 0.00 4.30
3210 10351 6.260050 TGATGCCCTACGATTTTGATAGTTTC 59.740 38.462 0.00 0.00 0.00 2.78
3215 10356 5.700832 GTGATGATGCCCTACGATTTTGATA 59.299 40.000 0.00 0.00 0.00 2.15
3225 10366 0.601311 GCTCGGTGATGATGCCCTAC 60.601 60.000 0.00 0.00 0.00 3.18
3229 10370 1.596477 GAGGCTCGGTGATGATGCC 60.596 63.158 0.00 0.00 43.52 4.40
3230 10371 0.879400 CAGAGGCTCGGTGATGATGC 60.879 60.000 9.22 0.00 0.00 3.91
3232 10373 1.332889 TGCAGAGGCTCGGTGATGAT 61.333 55.000 15.97 0.00 41.91 2.45
3233 10374 1.543944 TTGCAGAGGCTCGGTGATGA 61.544 55.000 15.97 0.00 41.91 2.92
3240 10381 2.684843 GGCTTGTTGCAGAGGCTCG 61.685 63.158 9.22 5.44 45.15 5.03
3241 10382 1.303155 AGGCTTGTTGCAGAGGCTC 60.303 57.895 6.34 6.34 44.45 4.70
3247 10388 0.317269 CAACACGAGGCTTGTTGCAG 60.317 55.000 16.61 4.11 45.36 4.41
3273 10414 0.456995 AAGACTCGTGCTAAGAGCGC 60.457 55.000 0.00 0.00 46.26 5.92
3278 10419 0.985549 GCGACAAGACTCGTGCTAAG 59.014 55.000 0.00 0.00 35.99 2.18
3280 10421 0.526211 ATGCGACAAGACTCGTGCTA 59.474 50.000 0.00 0.00 35.99 3.49
3281 10422 0.734253 GATGCGACAAGACTCGTGCT 60.734 55.000 0.00 0.00 35.99 4.40
3282 10423 1.687494 GGATGCGACAAGACTCGTGC 61.687 60.000 0.00 0.00 35.99 5.34
3283 10424 0.109086 AGGATGCGACAAGACTCGTG 60.109 55.000 0.00 0.00 35.99 4.35
3284 10425 0.171455 GAGGATGCGACAAGACTCGT 59.829 55.000 0.00 0.00 35.99 4.18
3285 10426 0.863538 CGAGGATGCGACAAGACTCG 60.864 60.000 0.00 0.00 41.20 4.18
3286 10427 0.526524 CCGAGGATGCGACAAGACTC 60.527 60.000 0.00 0.00 0.00 3.36
3287 10428 0.965866 TCCGAGGATGCGACAAGACT 60.966 55.000 0.00 0.00 0.00 3.24
3288 10429 0.103208 ATCCGAGGATGCGACAAGAC 59.897 55.000 3.45 0.00 32.98 3.01
3289 10430 1.609072 CTATCCGAGGATGCGACAAGA 59.391 52.381 14.50 0.00 36.17 3.02
3295 10436 3.608506 CGATAAAACTATCCGAGGATGCG 59.391 47.826 14.50 8.02 36.17 4.73
3313 10454 5.538118 ACCGCACATGAAAAGATATCGATA 58.462 37.500 7.75 7.75 0.00 2.92
3314 10455 4.380531 ACCGCACATGAAAAGATATCGAT 58.619 39.130 2.16 2.16 0.00 3.59
3316 10457 3.804325 AGACCGCACATGAAAAGATATCG 59.196 43.478 0.00 0.00 0.00 2.92
3318 10459 3.313526 GCAGACCGCACATGAAAAGATAT 59.686 43.478 0.00 0.00 41.79 1.63
3320 10461 1.470098 GCAGACCGCACATGAAAAGAT 59.530 47.619 0.00 0.00 41.79 2.40
3322 10463 3.389741 GCAGACCGCACATGAAAAG 57.610 52.632 0.00 0.00 41.79 2.27
3332 10473 0.110823 CAAACTACGTTGCAGACCGC 60.111 55.000 0.00 0.00 42.89 5.68
3333 10474 1.070843 CACAAACTACGTTGCAGACCG 60.071 52.381 0.00 1.58 31.29 4.79
3334 10475 1.937899 ACACAAACTACGTTGCAGACC 59.062 47.619 0.00 0.00 31.29 3.85
3344 10485 2.781646 GCACGAAAGCAACACAAACTAC 59.218 45.455 0.00 0.00 0.00 2.73
3381 10522 6.519382 CCTGACTAAGTCATCTGCAATATGA 58.481 40.000 7.20 7.20 41.94 2.15
3385 10526 3.054875 TGCCTGACTAAGTCATCTGCAAT 60.055 43.478 0.00 0.00 41.94 3.56
3389 10530 3.599730 TGTGCCTGACTAAGTCATCTG 57.400 47.619 0.00 0.00 41.94 2.90
3393 10534 1.339055 GCCATGTGCCTGACTAAGTCA 60.339 52.381 0.00 0.00 40.50 3.41
3395 10536 0.391661 CGCCATGTGCCTGACTAAGT 60.392 55.000 0.00 0.00 36.24 2.24
3398 10539 2.125147 GCGCCATGTGCCTGACTA 60.125 61.111 0.00 0.00 36.24 2.59
3406 10547 0.035881 ATCCCTCTATGCGCCATGTG 59.964 55.000 4.18 0.00 0.00 3.21
3407 10548 0.035881 CATCCCTCTATGCGCCATGT 59.964 55.000 4.18 0.00 0.00 3.21
3408 10549 1.303799 GCATCCCTCTATGCGCCATG 61.304 60.000 4.18 0.00 42.57 3.66
3409 10550 1.002868 GCATCCCTCTATGCGCCAT 60.003 57.895 4.18 0.63 42.57 4.40
3410 10551 2.427320 GCATCCCTCTATGCGCCA 59.573 61.111 4.18 0.00 42.57 5.69
3415 10556 7.756395 ATGTTTTTAGATGCATCCCTCTATG 57.244 36.000 23.06 0.00 0.00 2.23
3416 10557 8.773033 AAATGTTTTTAGATGCATCCCTCTAT 57.227 30.769 23.06 6.10 0.00 1.98
3417 10558 8.469200 CAAAATGTTTTTAGATGCATCCCTCTA 58.531 33.333 23.06 6.88 0.00 2.43
3418 10559 7.325694 CAAAATGTTTTTAGATGCATCCCTCT 58.674 34.615 23.06 7.97 0.00 3.69
3419 10560 6.036408 GCAAAATGTTTTTAGATGCATCCCTC 59.964 38.462 23.06 8.65 30.13 4.30
3420 10561 5.876460 GCAAAATGTTTTTAGATGCATCCCT 59.124 36.000 23.06 8.39 30.13 4.20
3421 10562 5.876460 AGCAAAATGTTTTTAGATGCATCCC 59.124 36.000 23.06 0.00 31.46 3.85
3422 10563 6.973229 AGCAAAATGTTTTTAGATGCATCC 57.027 33.333 23.06 7.23 31.46 3.51
3425 10566 6.699204 TCGAAAGCAAAATGTTTTTAGATGCA 59.301 30.769 0.00 0.00 30.93 3.96
3428 10569 9.346725 GAGATCGAAAGCAAAATGTTTTTAGAT 57.653 29.630 0.00 9.47 34.16 1.98
3429 10570 7.807907 GGAGATCGAAAGCAAAATGTTTTTAGA 59.192 33.333 0.00 0.00 30.93 2.10
3431 10572 6.866248 GGGAGATCGAAAGCAAAATGTTTTTA 59.134 34.615 0.00 0.00 30.93 1.52
3432 10573 5.696270 GGGAGATCGAAAGCAAAATGTTTTT 59.304 36.000 0.00 0.00 30.93 1.94
3434 10575 4.615912 CGGGAGATCGAAAGCAAAATGTTT 60.616 41.667 0.00 0.00 0.00 2.83
3436 10577 2.420022 CGGGAGATCGAAAGCAAAATGT 59.580 45.455 0.00 0.00 0.00 2.71
3437 10578 2.223340 CCGGGAGATCGAAAGCAAAATG 60.223 50.000 0.00 0.00 0.00 2.32
3438 10579 2.017049 CCGGGAGATCGAAAGCAAAAT 58.983 47.619 0.00 0.00 0.00 1.82
3439 10580 1.271163 ACCGGGAGATCGAAAGCAAAA 60.271 47.619 6.32 0.00 0.00 2.44
3440 10581 0.323629 ACCGGGAGATCGAAAGCAAA 59.676 50.000 6.32 0.00 0.00 3.68
3441 10582 0.323629 AACCGGGAGATCGAAAGCAA 59.676 50.000 6.32 0.00 0.00 3.91
3442 10583 0.391130 CAACCGGGAGATCGAAAGCA 60.391 55.000 6.32 0.00 0.00 3.91
3443 10584 0.108329 TCAACCGGGAGATCGAAAGC 60.108 55.000 6.32 0.00 0.00 3.51
3446 10587 1.509463 CGTCAACCGGGAGATCGAA 59.491 57.895 6.32 0.00 0.00 3.71
3447 10588 3.060020 GCGTCAACCGGGAGATCGA 62.060 63.158 6.32 0.00 36.94 3.59
3448 10589 2.582498 GCGTCAACCGGGAGATCG 60.582 66.667 6.32 10.57 36.94 3.69
3465 10606 6.620006 TGAAAATTAAAACGAAAACGCTTCG 58.380 32.000 16.21 16.21 46.36 3.79
3488 10629 8.586570 TGGTAGACAGTTGCAAAATAAAATTG 57.413 30.769 0.00 0.00 0.00 2.32
3489 10630 9.206870 CATGGTAGACAGTTGCAAAATAAAATT 57.793 29.630 0.00 0.00 0.00 1.82
3491 10632 7.946207 TCATGGTAGACAGTTGCAAAATAAAA 58.054 30.769 0.00 0.00 0.00 1.52
3493 10634 7.701539 ATCATGGTAGACAGTTGCAAAATAA 57.298 32.000 0.00 0.00 0.00 1.40
3494 10635 7.701539 AATCATGGTAGACAGTTGCAAAATA 57.298 32.000 0.00 0.00 0.00 1.40
3495 10636 6.594788 AATCATGGTAGACAGTTGCAAAAT 57.405 33.333 0.00 0.00 0.00 1.82
3497 10638 6.265196 AGAAAATCATGGTAGACAGTTGCAAA 59.735 34.615 0.00 0.00 0.00 3.68
3499 10640 5.181811 CAGAAAATCATGGTAGACAGTTGCA 59.818 40.000 0.00 0.00 0.00 4.08
3500 10641 5.634896 CAGAAAATCATGGTAGACAGTTGC 58.365 41.667 0.00 0.00 0.00 4.17
3501 10642 5.181811 TGCAGAAAATCATGGTAGACAGTTG 59.818 40.000 0.00 0.00 0.00 3.16
3503 10644 4.910195 TGCAGAAAATCATGGTAGACAGT 58.090 39.130 0.00 0.00 0.00 3.55
3504 10645 5.885230 TTGCAGAAAATCATGGTAGACAG 57.115 39.130 0.00 0.00 0.00 3.51
3505 10646 6.489700 TCTTTTGCAGAAAATCATGGTAGACA 59.510 34.615 0.00 0.00 30.59 3.41
3506 10647 6.913170 TCTTTTGCAGAAAATCATGGTAGAC 58.087 36.000 0.00 0.00 30.59 2.59
3508 10649 7.147312 TGTTCTTTTGCAGAAAATCATGGTAG 58.853 34.615 0.00 0.00 43.52 3.18
3509 10650 7.048629 TGTTCTTTTGCAGAAAATCATGGTA 57.951 32.000 0.00 0.00 43.52 3.25
3510 10651 5.916318 TGTTCTTTTGCAGAAAATCATGGT 58.084 33.333 0.00 0.00 43.52 3.55
3511 10652 6.847956 TTGTTCTTTTGCAGAAAATCATGG 57.152 33.333 0.00 0.00 43.52 3.66
3516 10657 9.558396 TGGATAATTTGTTCTTTTGCAGAAAAT 57.442 25.926 0.00 0.00 43.52 1.82
3521 10662 9.643693 AATACTGGATAATTTGTTCTTTTGCAG 57.356 29.630 0.00 0.00 0.00 4.41
3540 10681 6.751514 TGTACATACCTGCAAAAATACTGG 57.248 37.500 0.00 0.00 0.00 4.00
3572 10713 8.344098 AGACTTTTCTATTATCTTCGTCCTACG 58.656 37.037 0.00 0.00 44.19 3.51
3597 10738 8.737239 ACAAGATTTGGTCGGTGACGTTATAAG 61.737 40.741 0.00 0.00 45.16 1.73
3598 10739 7.015445 ACAAGATTTGGTCGGTGACGTTATAA 61.015 38.462 0.00 0.00 45.16 0.98
3599 10740 5.567224 ACAAGATTTGGTCGGTGACGTTATA 60.567 40.000 0.00 0.00 45.16 0.98
3600 10741 4.801581 ACAAGATTTGGTCGGTGACGTTAT 60.802 41.667 0.00 0.00 45.16 1.89
3601 10742 3.493002 ACAAGATTTGGTCGGTGACGTTA 60.493 43.478 0.00 0.00 45.16 3.18
3602 10743 2.743838 ACAAGATTTGGTCGGTGACGTT 60.744 45.455 0.00 0.00 45.16 3.99
3603 10744 1.202604 ACAAGATTTGGTCGGTGACGT 60.203 47.619 0.00 0.00 45.16 4.34
3604 10745 1.508632 ACAAGATTTGGTCGGTGACG 58.491 50.000 0.00 0.00 45.92 4.35
3605 10746 2.604614 GCAACAAGATTTGGTCGGTGAC 60.605 50.000 0.00 0.00 34.12 3.67
3606 10747 1.606668 GCAACAAGATTTGGTCGGTGA 59.393 47.619 0.00 0.00 34.12 4.02
3607 10748 1.336440 TGCAACAAGATTTGGTCGGTG 59.664 47.619 0.00 0.00 34.12 4.94
3608 10749 1.686355 TGCAACAAGATTTGGTCGGT 58.314 45.000 0.00 0.00 34.12 4.69
3609 10750 2.791383 TTGCAACAAGATTTGGTCGG 57.209 45.000 0.00 0.00 34.12 4.79
3610 10751 3.916172 CAGATTGCAACAAGATTTGGTCG 59.084 43.478 0.00 0.00 34.12 4.79
3611 10752 5.125100 TCAGATTGCAACAAGATTTGGTC 57.875 39.130 0.00 0.00 34.12 4.02
3612 10753 5.244402 TGATCAGATTGCAACAAGATTTGGT 59.756 36.000 0.00 0.00 34.12 3.67
3613 10754 5.716094 TGATCAGATTGCAACAAGATTTGG 58.284 37.500 0.00 0.00 34.12 3.28
3614 10755 6.387465 ACTGATCAGATTGCAACAAGATTTG 58.613 36.000 29.27 5.18 0.00 2.32
3624 10765 6.763135 GGTAAGATGTAACTGATCAGATTGCA 59.237 38.462 29.27 24.38 0.00 4.08
3673 10814 2.896745 TATGAGAGCATGCACGTGAT 57.103 45.000 22.23 7.22 35.94 3.06
3676 10817 3.490896 CGTTAATATGAGAGCATGCACGT 59.509 43.478 21.98 14.00 35.94 4.49
3682 10823 2.754472 TGCGCGTTAATATGAGAGCAT 58.246 42.857 8.43 0.00 38.54 3.79
3685 10826 3.555956 AGGTTTGCGCGTTAATATGAGAG 59.444 43.478 8.43 0.00 0.00 3.20
3688 10829 2.610374 GGAGGTTTGCGCGTTAATATGA 59.390 45.455 8.43 0.00 0.00 2.15
3692 10833 1.199097 CTTGGAGGTTTGCGCGTTAAT 59.801 47.619 8.43 0.00 0.00 1.40
3693 10834 0.589223 CTTGGAGGTTTGCGCGTTAA 59.411 50.000 8.43 0.02 0.00 2.01
3694 10835 0.249953 TCTTGGAGGTTTGCGCGTTA 60.250 50.000 8.43 0.00 0.00 3.18
3695 10836 0.889186 ATCTTGGAGGTTTGCGCGTT 60.889 50.000 8.43 0.00 0.00 4.84
3697 10838 1.425428 GATCTTGGAGGTTTGCGCG 59.575 57.895 0.00 0.00 0.00 6.86
3698 10839 1.803289 GGATCTTGGAGGTTTGCGC 59.197 57.895 0.00 0.00 0.00 6.09
3736 10877 7.239763 TCTAACAAGTGTCATGATGGACTAA 57.760 36.000 0.00 0.00 38.61 2.24
3741 10882 6.128172 GGAACTTCTAACAAGTGTCATGATGG 60.128 42.308 0.00 0.00 0.00 3.51
3742 10883 6.427853 TGGAACTTCTAACAAGTGTCATGATG 59.572 38.462 0.00 0.00 0.00 3.07
3743 10884 6.533730 TGGAACTTCTAACAAGTGTCATGAT 58.466 36.000 0.00 0.00 0.00 2.45
3745 10886 5.991606 TCTGGAACTTCTAACAAGTGTCATG 59.008 40.000 0.00 0.00 0.00 3.07
3746 10887 6.174720 TCTGGAACTTCTAACAAGTGTCAT 57.825 37.500 0.00 0.00 0.00 3.06
3767 10932 2.173996 GGGTAGCTCTCACTACTCCTCT 59.826 54.545 0.00 0.00 41.88 3.69
3770 10935 2.438800 TGGGTAGCTCTCACTACTCC 57.561 55.000 0.00 1.86 42.06 3.85
3771 10936 4.647399 AGAAATGGGTAGCTCTCACTACTC 59.353 45.833 0.00 0.00 42.90 2.59
3857 11022 7.683704 GCCGGAGTATATTCAGTAACTCAAGAA 60.684 40.741 5.05 0.00 40.09 2.52
3882 11047 1.520342 CTACCAAGCTGCTCTCGGC 60.520 63.158 1.00 0.00 44.91 5.54


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.